Ligand profile

C9D

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: KP13_06703 — Carbepenem-hydrolyzing beta-lactamase KPC2

Direct evidence PDB 6b1x UniProt Q9F663 Formula C₁₂H₂₁N₅O₇S
Mol. weight 379.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C9D
PDB
6b1x
UniProt (this protein)
Q9F663
Target protein
KP13_06703

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 379.40 Da
LogP (Crippen) -2.94
H-bond donors 5
H-bond acceptors 8
TPSA 166.17 Ų
Rotatable bonds 6
Aromatic rings 0 / 2
Heavy atoms 25
Fraction sp³ C 0.75
Formula C₁₂H₂₁N₅O₇S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 166.2
  • −1 ≤ LogP ≤ 5 -2.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 379.4
  • LogP ≤ 5 -2.94
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 166.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NNC(=O)[C@@H]2CCNC2
InChI 
InChI=1S/C12H21N5O7S/c18-7-17-6-9(16-24-25(21,22)23)1-2-10(17)12(20)15-14-11(19)8-3-4-13-5-8/h7-10,13,16H,1-6H2,(H,14,19)(H,15,20)(H,21,22,23)/t8-,9-,10+/m1/s1
InChIKey 
MPNPDELHXLJIKQ-BBBLOLIVSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00144' 'PF13354

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_06703.

PDB 35

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)